Wednesday, April 29, 2009

Today, there was a paper tangentially related to pterosaurs in the open access journal PLoS ONE. A team of investigators wired up albatrosses and petrels with accelerometers, in order to measure the percentage of time these animals spent flapping their wings and soaring. They found two main styles of wing flapping (as inferred from the accelerometer measurements): 1) high frequency flapping during take-off; and 2) low-frequency flapping during soaring. Interestingly, the frequencies scale with body mass in such a way that a maximum possible body size for the albatross-like body plan that still allows flight is extrapolated to a body mass of 41 kg and wingspan of 5.1 m (with the requisite error bars, of course).

The authors then go on to discuss the implications for pterosaur paleobiology, essentially suggesting that albatross-style soaring was physically impossible for pterosaurs such as Quetzlcoatlus (assuming that it also had albatross-style wings). Frustratingly, there is little discussion of the alternativepossibilitiesof wing shape in pterosaurs, among other things. Furthermore, the underlying data for the analysis only focus on four species of birds with limited morphological diversity. As suggested by the authors of the current paper, data on thermal-soaring birds such as condors (which have a decidedly un-albatross-like form) are sorely needed.

So, kudos to Sato et al. for collecting some interesting morphological data. This sort of information is invaluable for verifying and refining existing models of vertebrate flight. However, the relevance of the data to pterosaurs should probably be reviewed by someone who knows the group better than I do - so if you're one of those people, hop (or soar) on over to PLoS ONE and comment on the article!

We're almost to the end of the series on the 2009 Open Access Paleontology Journal Rankings (see other posts in the series here, here, and here)! Citations and number of papers are all well-and-good, but one thing that's often omitted in journal comparisons is community opinion. In other words, what do paleontologists think of this or that journal? Have they even heard of the journal?

In order to see how open access journals have fared within the paleontology community, I ran an informal survey. It provided a list of open access journals in paleontology, and asked respondents to rank each publication as "excellent," "good," "fair," "poor," or "I've never heard of it." This survey was advertised on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Ninety-two people responded, but not everyone answered every question. I have no idea (for the most part) who filled out the survey, but given the scope of advertising and the bits of feedback I received, I suspect respondents were primarily professional paleontologists and students of paleontology. Given the distribution of results, I have no reason to suspect poll crashing, but would also caution that this is not a scientifically sampled survey, either.

The results were then tallied, and an average rating was assigned to each. An excellent counted as 1 point, good as 2, fair as 3, poor as 4, and "never heard of it" as 5 points. So, here's the list from highest to lowest rating; the results are presented as"Journal Name, Average Score, (# Excellent Ratings, # Good Ratings, # Fair Ratings, # Poor Ratings, # Never Heard of It, Total Responses)." Journals with immediate open access are listed in bold.

NotesA low rating does not necessarily mean a journal for which paleontologists have a low opinion. In at least some cases (e.g., Palaeodiversity), low scores result largely from poor "brand recognition." As the crop of new journals matures, and as the internet allows broader distribution of work, this situation is likely to change.

Final ThoughtsIn hindsight, there are a few more things I'm curious about. How do major closed access journals such as JVPstack up against their open access brethern? Who responded to the survey, and how do different types of paleontologists (students, early career and late career professionals, etc.) consider open access journals versus their closed access counterparts? What are general attitudes amongst paleontologists towards open access?

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined previously). At the end of this series, I will post the raw data underlying the ratings.

Don't Forget The CaveatsRemember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Open Access Journals for Paleontology 2009 (General Results, Immediate and Delayed OA)

NoteIt should be noted that some very fine journals (e.g., PaleoBios) have open access archives for older issues (five years or older), but these publications were not included on the general list. I made the somewhat arbitrary decision to exclude journals with lag times of greater than one year.

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Yet Again With the CaveatsRemember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009 (General Results)

NotesIn some cases, relative ranks of journals may differ in this list from the previous category. This is because journals are ranked relative to all entries in a single category. For instance, PLoS ONE and PLoS Biologywere tied in the last list, but are separated in the present one. Let's consider the number of article citations - relative to all immediate open access journals, PLoS ONEis ranked fifteenth and PLoS Biologyis ranked second. When we exclude museum journals, the ratings move to ninth and second, respectively. When you add up all the rankings, little changes like this can jostle a journal's position; such behavior is particularly common near the top of the list. Later, I'll be releasing the underlying data and you can see for yourself.

Immediate Open Access Journals for General Submission (journals to which anyone can submit [excluding most museum publications with more exclusive author criteria], and which provide open access immediately upon publication)

All Open Access Journals (includes those journals with delayed open access)

Community Ranked Open Access Journals (journals as ranked by the opinions from the survey)

In this post, I'll just be covering Immediate Open Access Journals for General Submission. As described above, this includes only journals with immediate open access (versus open access after a set delay) and excludes those with restrictive authorship criteria (e.g., museum publications which usually require employment, association, or invitation to submit). The ratings are based on a combination of journal citations, recent citations, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Again With the CaveatsRemember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009 (General Submission)

NotesWhile compiling the results, I noted that sometimes community opinions of a journal varied from the rankings by sheer number of articles or citations. This will be highlighted in a future post. So, if you're worried because your favorite journal is lower than you thought, or your least favorite journal is higher than you thought, you'll probably be interested to see those results.

Unlike the widely-known Science Citation Index, these rankings include very new journals as well as more established journals. Thus, some rankings may change in the coming years are the new kids on the block accumulate more citations, more papers, and more exposure. Still, it is very interesting to note how some quite new journals (such as PLoS ONE) still have a high position within the list.

It is interesting to note how truly global this list is - a healthy mix of journals from South America, Europe, Asia, and North America round out the top 10. What does this mean, if anything, for the future of paleontology?

Friday, April 24, 2009

In a series of posts over the next several days, I will be releasing the long-awaited(?) rankings of open access journals. This post will provide some background on the journals, the ratings, and my methodology.

Why Rate Journals?Lots of open access journals are out there now--but not all are made equally. Some are widely read, others are ignored. Some publish high impact articles of general interest, and others are more focused in their scope. How is one to decide which publication to follow or submit research to? I've developed these ratings primarily as a service to those of us who are looking for open access journals in which to publish. Rankings that incorporate citation counts, numbers of articles published, and community opinion may be useful as one part of this decision-making progress.

How Were the Journals Chosen?Basically, I combed the internet, dredged up my own knowledge of the literature, used the list on SV-POW!, and incorporated comments from readers. I have quite probably omitted one or two journals by accident, and I can assure you that this was unintentional. I adopted four criteria for selecting journals:

The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).

Entire issues must be open access, not just selected articles.

The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).

The journal may have either immediate or delayed open access (a year is the cut-off point).

How Were the Journals Rated?Journals were evaluated in five general areas:

Number of journal hits. This was calculated by searching for all articles within a given journal on Google Scholar, and recording the number of hits. [example]

Number of paleontology hits. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of hits. [example]

Number of article citations. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of citations for the top 10 search results. [example]

Number of citations of recent articles. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," published in 2007 or 2008, and recording the number of citations for the top 10 search results. [example]

Community rating. A survey was posted with a list of all journals, and respondents were invited to rate each journal as "excellent," "good," "fair," "poor," or "never heard of it." A notice of the survey was posted on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Each journal was then given an overall rating, by weighting the number of responses in each category.

The journals were ranked in each category, and then an overall ranking incorporating all categories was calculated.

A DisclaimerThese are informal ratings, compiled in a manner that is probably non-scientific and flawed in one or more ways. No ranking system is perfect! Regardless of any imperfections, I think that these rankings may provide some useful information. Just take it with a grain of salt.

Thursday, April 23, 2009

Another high profile journal has made its first steps towards open access! I learned earlier today that Sciencenow has free access to its archives, for articles older than one year and published on or after January 1997. Registration (free) is required, but this is quick and relatively painless.

Unfortunately, it is too late to add Science to the survey, but it will be included in other ranking methods. If you haven't already, don't forget to fill out the open access journal poll! It closes Friday night, 23 April.

[Note: I also learned that the journal has actually had open archives for since 2001 - wow, am I out of the loop!]

Saturday, April 18, 2009

The number of open access journals available for paleontologists is growing rapidly (see both my previous post as well as a more comprehensive post over at SV-POW!). When it comes time to submit something for publication, the options can be quite disconcerting. What journal will best get that paper out there? Search engines are great for finding specific papers on a specific topic, but it's nice to know that the casual journal reader might also happen across your paper. So, which journals do my colleagues pay attention to? Which journals do my colleagues respect most?

Although inherently flawed in some respects, ranking systems provide a first pass at trying to evaluate publications. So, I've been working on developing a rudimentary ranking system for today's open access paleontology journals. And, I'd like your help! I'll be incorporating citation counts, page rankings, and other metrics, but would also like to consider reader opinion. So, I have developed a highly unscientific survey as part of this effort. Please take a few minutes to fill in your opinions.

As a preview, the survey provides a list of open access journals in paleontology, and asks you to rank them as "excellent," "good," "fair," "poor," or "I've never heard of it." The form will be open until next Friday evening at 11:45 (Pacific time). Results will be published here soon thereafter.

Coming Up, After Your Hard Work on the Poll: The Top Open Access Journals for Paleontology 2009.

Thursday, April 16, 2009

As part of a larger upcoming post (by the weekend, I hope), I am compiling a list of open access journals that regularly publish articles in paleontology. So far, the journals have been selected using the following criteria:

1) The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).2) Entire issues must be open access, not just selected articles.3) The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).4) The journal may have either immediate or delayed open access (a year is the cut-off point).

Here's what I have so far. . .any suggestions for additions or corrections? At this point, I am not making statements one way or another on the quality of the journals. . .just assembling a list!

Saturday, April 4, 2009

With more journals accessible than ever before, drinking from the stream of knowledge is more like chugging from the fire hydrant of information. Jerry Harris lists over 300 journals that publish vertebrate paleontology-relevant content. . .and the number is increasing all the time! With papers ranging from the obscure to the earth-shaking, it's both an overwhelming and important task to keep on top of the literature.

Fortunately, the same resources that create this flood of information also offer some life rafts to stay afloat. In this post, I'll cover a few tips, tricks, and tools that I use to stay "in the know" on paleontology.

Journal Subscriptions. If you're a paleontologist (avocational, professional, or otherwise) or paleontological enthusiast, you should be subscribing to one or two of the major journals in the field as part of your professional memberships (e.g., Society of Vertebrate Paleontology, Palaeontological Association, Paleontological Society). These will get you the earliest and easiest access to many of the most important articles in the field. Warning: Rant Ahead! Look - if you're seriously interested in paleontology, you need to join one of these societies. Not only do you get to support organizations that are doing good things in the name of paleontology, but you get journal access (print and/or online) as part of the package deal. And, they're really, truly not that expensive. I was a poor student once myself (and am still not what would be considered rich), but let's get real, folks. A student membership for SVP costs only $70 a year. Yes, I know that's real money. . .but it's also not much more than that copy of Halo 3 that you bought, or that history textbook you'll never read, that cable TV subscription you don't need, or the amount you spent on beer (or bottled water, or soda, or coffee, or energy drinks, or whatever your overpriced beverage of choice is) last month. An associate membership in SVP is but $50 (online access to the journal only, but a viable option for those folks who aren't students and/or don't think they will attend one of the annual meetings), and full membership is $140. Seriously - in most cases (and I recognize that there are some exceptions based on personal circumstances - you folks know who you are), there are no excuses for not joining at least one professional society. Start saving your pennies now, because it's an investment in your future as a paleontologist. (ok, my rant is over)

Paleontology Mailing Lists. One of the few (in my opinion) remaining uses for the Dinosaur Mailing List is publication alerts posted by some generous members (in particular, Jerry Harris). These alerts often scrape together valuable papers from obscure or hard-to-find journals. The downside with subscribing is that you also get a blizzard of emails on how T. rex could best a pack of Spinosaurus, PDF requests, and the inevitable "that species name isn't spelled correctly" postings.

Journal Web Pages. Most journals (at least, journals worth their salt) have web pages with listings of current content. So, you can always just browse on over, and see what this month's articles bring. Of course, this gets really old if there are more than about three journals to keep track of, and it's easy to forget. So, how about trying. . .

Journal RSS Feeds. Some journals, such as Palaeontology, have RSS feeds available. These can be really handy, but again overwhelming if you really want to check on a whole host of journals. So, this brings us to. . .

Journal Content Alerts. This is my personal favorite method for keeping updated on the latest and greatest papers. Many publishers and journal bundlers (including Wiley, Evilsevier, BioOne, PLoS, and others) allow you to sign up for free content alerts. So, when a new issue is published, you get a little email with a listing of every article in there. It's kinda like the old-fashioned technique of going to the journal stacks and thumbing through all of the recent issues, except you can do it in your pajamas without funny looks from librarians. As an added bonus, you often can set up searches for alerts whenever a topic of interest, like "dinosaur," shows up in any journal across the publisher's collection. This sometimes results in irrelevant papers (childhood education articles come up frequently), but it also might get you interesting hits from journals that you might not follow otherwise (e.g., respiratory physiology). I've set up a dedicated email account (thanks, Gmail!) just for this purpose.

About the Blog

Ramblings on the role of open source software and open access publishing in paleontology, the latest and sometimes not-so-greatest ways in which we reconstruct the past, and the occasional bits of career advice and paleo news.

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This is a personal weblog, and the opinions expressed here represent my own and not those of my employer or any other organization with which I am associated. Although I strive for accurate information, please be aware that the advice offered here is "as is," with no claims or guarantees that it will work for you. Hey, I'm just a paleontologist.